Tag Archives: resource update

Video Tip of the Week: the New PubMed Filters Sidebar

In today’s tip I am linking to a YouTube video from NCBI that briefly explains the new Filters Sidebar feature that has been added to PubMed. We first saw a tweet that the change was coming back on May 2nd, just as I was completing a total update to our full PubMed tutorial*.

I struggled with whether to hold our production team for the new sidebar, or to produce our tutorial with the plan to update in the near future – it is always a struggle to know which is the best option because resource changes can occur at the speed of light, or according to geological time scales (ok, that’s an exaggeration but it feels that way when you want to release a wonderful, up-to-date project & something holds you up and causes delayed publication of our tutorial materials). With PubMed I was lucky – I saw a tweet that the sidebar feature would be added “in the next week”. I asked our voice professional to put the script on hold & I paced around PubMed waiting to see what (& when) things would occur.

True to their word, the sidebar feature showed up on PubMed results on May 10th, exactly one week since I had seen the “in the next week” announcement – my THANKS to the NCBI & PubMed Teams! :) Not only did they push out their updates in a timely manner, they made a YouTube video explaining the changes & discussing where future changes are slated to go. The video is clear, and quick, so I am using it as my tip this week. I’m not sure the feature is 100% stable, as I show in the image below, and describe later in the post, but I think the change might accomplish NCBI’s goal – for more people to notice & utilize filters for their searches.

In the video the narrator states that the filters area is gone & the two default filters are permanently selected, as indicated by the check marks that can’t be “unclicked”. I”m not seeing those check marks on either “Free full text available” link (shown) or the “Review” link, which is not in view in my image. I also see a difference as to whether I get the right filtered subsets depending on whether I am logged into My NCBI (the upper window shown in the back of the image), or not (the lower, front window). In my hands IE 9.0 & Firefox 12.0 both function similarly in these aspects.

The NCBI video doesn’t really show how results look after filters are added, but in playing with it to me it looks like all of your filters are applied to your search & you only get one set of results, not links to various subsets. Although it is now easier to add filters to searches, if that’s how filters are going to work going forward, I think I will miss the old filters – I kind of like being able to switch between various subcategories of results without having to change my filters or rerun searches. Be sure to share your thoughts & preferences with NCBI so that they can create the best resource for their users needs!

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick links:

OpenHelix Introductory Tutorial on using PubMed (soon to be updated): http://www.openhelix.com/cgi/tutorialInfo.cgi?id=70

PubMed Resource: http://www.pubmed.gov/

PubMed Reference:
Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S. & (2011). Database resources of the National Center for Biotechnology Information, Nucleic Acids Research, 40 (D1) D25. DOI: 10.1093/nar/gkr1184

Many Protein Resources Have Recently Announced Updates

PDB structure 3rg9

 

 

 

 

In our ongoing pursuit of up-to-date tutorials, I’ve been tracking changes that are occurring at resources and planning our updates accordingly. Protein resources are especially going to keep me out of trouble this summer, because their developers and curators have been busy! I’ve compiled a short synopsis below, and would appreciate comments on any other resources you know about, or want to brag about! :)

  • I featured the ExPASy list of proteomic tools in a past tip. As of  Tuesday this list is no longer being kept up-to-date, but the ExPASy resource has been expanded beyond being “just” a proteomics resource and is now the new SIB Bioinformatics Resource Portal. According to its developers, the portal:

    “provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. … On this portal you find resources from many different SIB groups as well as external institutions.”

    And never fear, there is still an up-to-date list of proteomics tools found here.

  • I mentioned in my tip last week that NCBI’s MMDB has undergone an update & I’ll be updating our tutorial on it soon.
  • NCI/Nature Pathway Interaction Database, or PID, had an update June 14th that includes new and updated pathway information.
  • PROSITE had an update June 21st, which is Release 20.73, and now includes 1618 documentation entries, 1308 patterns, 936 profiles and 925 ProRules.
  • The RCSB PDB resource has announced updates to their Browse Database function, enhanced sequence displays from structure summary pages and the PDB-101 educational resource available from blackboard logos on PDB pages. For more details on using PDB, please see our free PDB Introductory tutorial sponsored by the RCSB.
  • STRING’s 9.0 release is now available, and we’ll be looking into anything we need to update in our tutorial as a result.
  • UniProt released an update June 28th that included a major update on many bacterial and archaeal Type II Toxin-Antitoxin modules, as is described here.

Enjoy all the new information – I know I will! :)

Tip of the Week: Introduction to Changes to NCBI’s Protein Database


In today’s tip I will introduce you briefly to the changes at NCBI’s Protein database. I highlighted that changes had been made in a Friday SNPets, and someone asked for more details. Our full updated tutorial will be much more complete than this short tip, so be watching for that to be completed in the near future – but for now, enjoy this tip & head over to NCBI to do some exploring of your own!